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A MediaWiki implementation of single-access keys

Gregor Hagedorn, Bob Press, Sonia Hetzner, Andreas Plank, Gisela Weber, Sabine von Mering,

Stefano Martellos, Pier Luigi Nimis

Abstract — Design principles, features, and data exchange options of an open source implementation of single access keys for the collaborative MediaWiki platform are presented.

Index Terms — field guides, flora, fauna, identification tools, KeyToNature, social software, SDD, MediaWiki, single-access key, dichotomous key, polytomous key.

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1 introduction

Among the various forms of computer-aided identification keys (compare [1], [2]), single-access keys have long been neglected, being studied pri-marily as a printable output from character × taxon matrices. However,

single-access keys may also be used interactively. Examples are Lucid Phoenix [3] (commercial), Frida/Dryades [4] (closed source), and the two KeyToNature open source projects: Open Key Editor [5] and biowikifarm [6] “Wiki keys”. The latter implementation, based on JavaScript enhanced Media Wiki [7] templates, is presented here in detail. Its strength is the integration into the collaborative MediaWiki software with much broader applicabi lity for developing floras, faunas or field guides.

2 deSign principleS

Much of the strength of single access keys derives from information re duc tion. The information which is actually used in the key (and which must be understood by the user) is only a fraction of the total information pre sent in the descriptions of the taxa.

————————————————G. Hagedorn, A. Plank, G. Weber, S. v. Mering are with the Julius Kühn-Institute, Federal Re-search Centre for Cultivated Plants, Inst. for Epidemiology and Pathogen Diagnostics, Königin-Lu-ise-Str. 19, D-14195 Berlin, E-mail: gregor.hagedorn@jki.bund.de. – Bob Press is with the Natural History Museum London – S. Hetzner is with the Inst. f. Lern-Innovation, Universität Erlangen-Nürnberg, D-91052 Erlan gen – S. Martellos, P. L. Nimis are with the Dept. of Life Sciences, University Trieste, I-34127, Trieste, Italy. E-mail: nimis@units.it, martelst@units.it.

Nimis P. L., Vignes Lebbe R. (eds.) Tools for Identifying Biodiversity: Progress and Problems – pp. 77-82.ISBN 978-88-8303-295-0. EUT, 2010.

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In a perfect world with an unlimited number of characters that are con venient and reliable to observe, monomorphic (not variable within spe cies), available for observation at all times, and splitting the remaining taxa into evenly sized partitions, the most reduced identification keys would be the best. In the real world, however, the various imperatives for character selection are in conflict. The resulting keys often use character combinations instead of single characters and may provide verification characters that are not strictly necessary. Similarly, several suboptimal illustrations may be necessary to understand character variability.

Fig. 1 – A Wiki key [8] as part of a wiki page, presented in overview mode (“Step-by-step identification” starts the interactive mode), and with part of the information hidden (“more…” will display the hidden information). The key metadata (Geographic Scope

following) are initially displayed, but hideable.

Fig. 2 – A variant wiki template generates a horizontal (side-by-side) layout. Both the horizontal and vertical layout can be used interactively and both provide for sub-

headings (“Tail yellow-white”, etc.).

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Fig. 3 – Extra information is initially hidden (top). It will be displayed (bottom) after clicking on “more…”.

In the MediaWiki single-access keys, initially only terse lead statements (which should be limited to information strictly complementary within a couplet) and a subset of images are shown (in standard layout, Fig. 1, small previews in a margin plus up to 2 larger images below each lead; in horizontal layout, Fig. 2, up to 8 images above the lead statement).

As a form of “information reduction management”, further information is shown only on request: general remarks, a gallery of up to 8 secondary illus trations, and – for taxa – synonyms, brief diagnosis, occurrence, distri bu tion, and habitat information (Fig. 3).

All images are displayed at a reduced size, sufficient only to enable the user to decide if enlarging is worthwhile. The zoom functionality acts in the page context (Fig. 4). It further provides a link to creator, copyright, and license information, required to be directly accessible by many licenses.

Information hiding is implemented through JavaScript in a graceful de gra-dation design (i. e. without JavaScript, no information is hidden).

Fig. 4 – Enlarged image as an overlay to the page.

At the bottom an image caption and a link to the IPR infor mation (legally required by the Creative Commons

licen ses) is provided.

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Fig. 5 – Wiki key in JavaScript-based interactive mode. The history of previous decisions is displayed at the bottom, with decision 3 having been marked as uncertain.

Fig. 6 – Steps in the history or previous decisions are revisable (here step 4 is being revised). Later steps are confirmable and discarded only if a conflicting decision is

taken.

3 Interactive step-by-step identification

The printable overview can be switched to an interactive mode. The open source jKey player [9] then displays only a single choice at a time (Fig. 5), helping esp. students to concentrate. To maintain context, a history of pre vious decisions is provided. Steps are revisable, maintaining pro gress as long as possible (Fig. 6). The history also helps to verify identifi cations, since it can be read as a description of the object that is being identified.

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Fig. 7 – Display of a glossary definition in an overlay on the web page (not in a separate window).

Fig. 8 – After selecting the button: “Undecided: try all alternatives”, multiple alternative paths may be followed.

4 data exchange

The KeyToNature-Dryades/Frida system provides a special export format that directly creates text formatted to be pasted into wiki pages as ready wiki text. Wiki keys can further be converted to SDD xml data by a con verter created at the Natural History Museum in London.

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5 pedagogical featureS

The single-access keys are supported by several pedago gi cally relevant features:

1. Illustrated concept definitions and help pages, stored as editable wiki pages, may be accessed from any point in the identification key, providing context-sensitive help. When the user hovers the mouse over a term, the defini tion opens in a pop-up layer (Fig. 7). From there a new window can be opened if needed.

2. The history allows direct access to and revision of any previous deci-sion. This may occur in a dialogue with the teacher, who can help in re view ing misinterpretations.

3. Users can flag particular decisions as “uncertain” (Fig. 5). Although this does little more than marking a step in the history, it can greatly en hance the student-teacher communication. It allows students to ac tively seek teacher assistance at a time when he or she is available, while con tinuing their work in the meantime.

4. The interactive mode offers an option to not take a decision at a given step, allowing users to explore the key in multiple directions. After selecting the “Undecided: try all alternatives” button, the player will con tinue with the first alternative. However, the history allows the user to switch between alternative branches, recording in all branches (Fig. 8).

acknowledgement

This work was supported by the KeyToNature Project, ECP-2006-EDU-410019, in the eContentplus Programme.

referenceS

[1] R. J. Pankhurst, Practical Taxonomic Computing, 1991.[2] G. Hagedorn, G. Rambold and S. Martellos 2010, “Types of identification keys”. In: P. L. Nimis

and R. Vignes Lebbe (eds.), Tools for Identifying Biodiversity: Progress and Problems, pp. 59-64, 2010.

[3] Lucid Phoenix (http://www.lucidcentral.org/LinkClick.aspx?link=152), 2010-07.[4] S. Martellos and P. L. Nimis, “KeyToNature: Teaching and Learning Biodiversity. Dryades,

the Italian Experience.” In: M. Muñoz, I. Jelìnek, F. Ferreira (eds.), Proceedings of the IASK Interna tional Conference Teaching and Learning 2008, pp. 863-868, 2008.

[5] S. Martellos, E. v. Spronsen, D. Seijts, N. Torrescasana Aloy, P. Schalk and P. L. Nimis, “User-generated content in the digital identification of organisms: the KeyToNature approach” Int. J. Information and Operations Management Education, vol. 3, 3, pp. 272-83, 2010.

[6] MediaWiki software, http://www.mediawiki.org/wiki/MediaWiki, 2010-07.[7] G. Hagedorn, G. Weber, A. Plank, M. Giurgiu, A. Homodi, C. Veja, G. Schmidt, P. Mihnev, M.

Roujinov, D. Triebel, R. A. Morris, B. Zelazny, E. van Spronsen, P. Schalk, C. Kittl, R. Brandner, S. Martellos and P. L. Nimis, “An online authoring and publishing platform for field guides and identifi ca tion tools”. In: Nimis P. L. Nimis and R. Vignes Lebbe (eds.), Tools for Identifying Biodiversity: Progress and Problems, pp. 13-18, 2010.

[8] B. Press, Key to common UK street trees. http://www.keytonature.eu/wiki/Key_to_common_UK_street_trees, 2010-07.

[9] S. Opitz and G. Hagedorn, “The jKey wiki key player and builder”. Proc. of TDWG 2009, pp. 9-13 Nov. 2009, Montpellier, 2009.